Spatial interplay of lymphocytes and fibroblasts in estrogen receptor-positive HER2-negative breast cancer.

In estrogen-receptor-positive, HER2-negative (ER+HER2-) breast cancer, higher levels of tumor infiltrating lymphocytes (TILs) are often associated with a poor prognosis and this phenomenon is still poorly understood. Fibroblasts represent one of the most frequent cells in breast cancer and harbor immunomodulatory capabilities. Here, we evaluate the molecular and clinical impact of the spatial patterns of TILs and fibroblast in ER+HER2- breast cancer. We used a deep neural network to locate and identify tumor, TILs, and fibroblasts on hematoxylin and eosin-stained slides from 179 ER+HER2- breast tumors (ICGC cohort) together with a new density estimation analysis to measure the spatial patterns. We clustered tumors based on their spatial patterns and gene set enrichment analysis was performed to study their molecular characteristics. We independently assessed the spatial patterns in a second cohort of ER+HER2- breast cancer (N = 630, METABRIC) and studied their prognostic value. The spatial integration of fibroblasts, TILs, and tumor cells leads to a new reproducible spatial classification of ER+HER2- breast cancer and is linked to inflammation, fibroblast meddling, or immunosuppression. ER+HER2- patients with high TIL did not have a significant improved overall survival (HR = 0.76, P = 0.212), except when they had received chemotherapy (HR = 0.447). A poorer survival was observed for patients with high fibroblasts that did not show a high level of TILs (HR = 1.661, P = 0.0303). Especially spatial mixing of fibroblasts and TILs was associated with a good prognosis (HR = 0.464, P = 0.013). Our findings demonstrate a reproducible pipeline for the spatial profiling of TILs and fibroblasts in ER+HER2- breast cancer and suggest that this spatial interplay holds a decisive role in their cancer-immune interactions.

Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector. Corrigendum.

Corrections are made to Table 1 in the article by van Genderen et al. [Acta Cryst. (2016), A72, 236-242].

A full-term healthy neonate with respiratory distress.

Pneumopericardium, defined as air in the pericardial cavity, is a rare condition with potentially severe complications and mortality. In the neonatal period, pneumopericardium is associated with prematurity, very low birth weight, and assisted ventilation. We report the occurrence of spontaneous pneumopericardium in a healthy full-term neonate who did not receive any supportive ventilation.

The seed to success: The role of seminal plasma in pregnancy.

A lack of immunologic tolerance of the mother toward her child and in placentation can result in early or late pregnancy complications, including implantation failure, miscarriage, preeclampsia, and fetal growth restriction. Seminal plasma has the potential of influencing the maternal immune system for acceptance of the semi-allogeneic fetus. Here we elaborate on studies which provide evidence that an optimal balance of pro-inflammatory and immunomodulatory factors is necessary for the induction of immunologic tolerance and the process of implantation and placentation. Seminal plasma is a source of immunological mediators at conception, which can influence the function of maternal immune cells. Identifying the relevant factors in seminal plasma and the mechanisms by which they affect the maternal reproductive tract in relation to pregnancy outcome is a challenge for future research.

Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector.

Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼ 0.013 e(-) Å(-2) s(-1)) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014).

Lattice filter for processing image data of three-dimensional protein nanocrystals.

When 300 kV cryo-EM images at Scherzer focus are acquired from ∼ 100 nm thick three-dimensional protein nanocrystals using a Falcon 2 direct electron detector, Fourier transformation can reveal the crystalline lattice to surprisingly high resolutions, even though the images themselves seem to be devoid of any contrast. Here, it is reported how this lattice information can be enhanced by means of a wave finder in combination with Wiener-type maximum-likelihood filtering. This procedure paves the way towards full three-dimensional structure determination at high resolution for protein crystals.